Config appendconfig + saving + logging

[sonninnos]

Description

This tackles a few config related issues:

• Allows use of --appendconfig with override cfgs instead of getting ignored
• No more console startup logging if logging to file
• Saves config on exit only once instead of 3 times by
  • Making sure retroarch_main_quit() isn't called many times at once where possible, and also by doing saving depending on shutdown flag to prevent it from firing more than once
  • Removing saving from main_exit()

Also some indentation corrections and nits.

Related Issues

Closes #9007
Closes #5457